LitCovid-sentences  

PMC:7172841 / 26462-34599 JSONTXT 12 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T188 0-12 Sentence denotes STAR★Methods
T189 14-33 Sentence denotes Key Resources Table
T190 34-71 Sentence denotes REAGENT or RESOURCE SOURCE IDENTIFIER
T191 72-82 Sentence denotes Antibodies
T192 83-151 Sentence denotes CD14-FITC (RMO52 clone) Beckman Coulter Cat#IM0645U; RRID: AB_130992
T193 152-219 Sentence denotes CD45-PC5 (J33 clone) Beckman Coulter Cat#IM2653U; RRID: AB_10641226
T194 220-289 Sentence denotes HLA-DR-RD1 (9-49 clone) Beckman Coulter Cat#6604366; RRID: AB_2832962
T195 290-375 Sentence denotes IgG1-PE isotype control (679.1Mc7 clone) Beckman Coulter Cat#A07796; RRID: AB_2832963
T196 376-463 Sentence denotes IgG1-FITC isotype control (679.1Mc7 clone) Beckman Coulter Cat#A07795; RRID: AB_2832964
T197 464-564 Sentence denotes CD3-FITC/CD4-PE Antibody Cocktail (UCHT1/13b8.2 clones) Beckman Coulter Cat#A07733; RRID: AB_2832965
T198 565-643 Sentence denotes CD3-FITC/CD8-PE Antibody Cocktail Beckman Coulter Cat#A07734; RRID: AB_2832966
T199 644-753 Sentence denotes CD3-FITC/CD(16+56)-PE Antibody Cocktail (UCHT1/3G8/N901 (NKH-1)) Beckman Coulter Cat#A07735; RRID: AB_1575965
T200 754-834 Sentence denotes CD19-FITC/CD5-PE Antibody Cocktail Beckman Coulter Cat#IM1346U; RRID: AB_2832967
T201 835-927 Sentence denotes Quantibrite Anti-HLA-DR/Anti-Monocyte (L243/MϕP9) BD Biosciences Cat#340827; RRID: AB_400137
T202 928-1008 Sentence denotes Mouse Anti-Human IL-6-PE (AS12 clone) BD Biosciences Cat#340527; RRID: AB_400442
T203 1009-1054 Sentence denotes Chemicals, Peptides, and Recombinant Proteins
T204 1055-1103 Sentence denotes VersaLyse Lysing Solution Beckman Coulter A09777
T205 1104-1144 Sentence denotes Fixative Solution Beckman Coulter A07800
T206 1145-1208 Sentence denotes eBioscience™ Brefeldin A Solution (1000x) Invitrogen 00-4506-51
T207 1209-1266 Sentence denotes IntraPrep Permeabilization Reagent Beckman Coulter A07802
T208 1267-1325 Sentence denotes RPMI 1640 W/ Stable Glutamine W/ 25 MM HEPES Biowest L0496
T209 1326-1378 Sentence denotes Lymphosep, Lymphocyte Separation Media Biowest L0560
T210 1379-1460 Sentence denotes PBS Dulbecco’s Phosphate Buffered Saline w/o Magnesium, w/o Calcium Biowest L0615
T211 1461-1534 Sentence denotes FBS Superior; standardized Fetal Bovine Serum, EU-approved Biochrom S0615
T212 1535-1588 Sentence denotes Gentamycin Sulfate BioChemica PanReac AppliChem A1492
T213 1589-1651 Sentence denotes Penicillin G Potassium Salt BioChemica PanReac AppliChem A1837
T214 1652-1720 Sentence denotes Lipopolysaccharides from Escherichia coli O55:B5 Sigma-Aldrich L2880
T215 1721-1747 Sentence denotes Critical Commercial Assays
T216 1748-1793 Sentence denotes Human IL-1β uncoated ELISA Invitrogen 88-7261
T217 1794-1839 Sentence denotes Human TNF-α uncoated ELISA Invitrogen 88-7346
T218 1840-1875 Sentence denotes Human IL-6 ELISA Invitrogen 88-7066
T219 1876-1934 Sentence denotes Human IL-17A (homodimer) uncoated ELISA Invitrogen 88-7176
T220 1935-1989 Sentence denotes Human Ferritin ELISA ORGENTEC Diagnostika GmbH ORG 5FE
T221 1990-2028 Sentence denotes Human IFN-γ ELISA Diaclone 950.000.192
T222 2029-2052 Sentence denotes Software and Algorithms
T223 2053-2110 Sentence denotes GraphPad Prism Graphpad Software https://www.graphpad.com
T224 2111-2174 Sentence denotes SPSS IBM https://www.ibm.com/analytics/spss-statistics-software
T225 2176-2197 Sentence denotes Resource Availability
T226 2199-2211 Sentence denotes Lead Contact
T227 2212-2349 Sentence denotes Further information and requests for resources and reagents should be directed to and will be fulfilled by the Lead Contact, Evangelos J.
T228 2350-2396 Sentence denotes Giamarellos-Bourboulis (egiamarel@med.uoa.gr).
T229 2398-2420 Sentence denotes Materials Availability
T230 2421-2469 Sentence denotes This study did not generate new unique reagents.
T231 2471-2497 Sentence denotes Data and Code Availability
T232 2498-2573 Sentence denotes Data of this study are available after communication with the Lead Contact.
T233 2575-2613 Sentence denotes Experimental Model and Subject Details
T234 2614-2759 Sentence denotes Blood was sampled from patients with CAP and sepsis and CAP by SARS-CoV-2 of either gender within the first 24 h of hospital admission (Table 1).
T235 2760-2971 Sentence denotes CAP was defined as the presence of new infiltrate in chest X-ray in a patient without any contact with any healthcare facility the last 90 days; sepsis was defined by the Sepsis-3 criteria (Singer et al., 2016).
T236 2972-3125 Sentence denotes COVID was diagnosed for patients with CAP confirmed by chest X-ray or chest computed tomography and positive molecular testing of respiratory secretions.
T237 3126-3255 Sentence denotes For patients who required MV, blood sampling was performed within the first 24 h from MV and results were used for this analysis.
T238 3256-3476 Sentence denotes Exclusion criteria were infection by the human immunodeficiency virus; neutropenia; and any previous intake of immunosuppressive medication (corticosteroids, anti-cytokine biologicals, and biological response modifiers).
T239 3477-3589 Sentence denotes SRF was defined as severe decrease of the respiratory ratio necessitating intubation and mechanical ventilation.
T240 3590-3864 Sentence denotes The studies were conducted under the 78/17 approval of the National Ethics Committee of Greece; the 23/12.08.2019 approval of the Ethics Committee of Sotiria Athens General Hospital; and the 26.02.2019 approval of the Ethics Committee of ATTIKON University General Hospital.
T241 3865-3982 Sentence denotes Written informed consent was provided by patients or by first-degree relatives in case of patients unable to consent.
T242 3983-4151 Sentence denotes All data of patients with bacterial CAP screened for participation in the randomized clinical trial with the acronym PROVIDE (ClinicalTrials.gov NCT03332225) were used.
T243 4152-4256 Sentence denotes All patients admitted for CAP by SARS-CoV-2 from March 3 until March 30, 2020 participated in the study.
T244 4257-4338 Sentence denotes No randomization to experimental groups was needed according to the study design.
T245 4340-4354 Sentence denotes Method Details
T246 4355-4608 Sentence denotes White blood cells were incubated for 15 min in the dark with the monoclonal antibodies anti-CD14 FITC, anti-HLA-DR-PE, anti-CD45 PC5 (Beckman Coulter, Marseille, France) and Quantibrite HLA-DR/anti-monocyte PerCP-Cy5 (Becton Dickinson, Cockeysville Md).
T247 4609-4936 Sentence denotes White blood cells were also incubated for 15 min with anti-CD3 FITC, anti-CD4 FITC and anti-CD19 FITC (fluorescein isothiocyanate, emission 525 nm, Beckman Coulter); with anti-CD4 PE, anti-CD8 PE, and anti-CD(16+56) PE (phycoerythrin, emission 575nm, Beckman Coulter); and with anti-CD45 PC5 (emission 667 nm, Beckman Coulter).
T248 4937-5020 Sentence denotes Fluorospheres (Beckman Coulter) were used for the determination of absolute counts.
T249 5021-5134 Sentence denotes Cells were analyzed after running through the CYTOMICS FC500 flow cytometer (Beckman Coulter Co, Miami, Florida).
T250 5135-5212 Sentence denotes Isotypic IgG controls stained also with anti-CD45 were used for each patient.
T251 5213-5315 Sentence denotes Results were expressed as absolute molecules of HLA-DR on CD14/CD14+CD45+ cells, percentages, and MFI.
T252 5316-5623 Sentence denotes In separate experiments, whole blood was treated with 10 μg/mL brefeldin A (Invitrogen, Carlsbad, CA, USA) for 60 min at 37°C in 5% CO2 followed by incubation in the dark for 15 min at room temperature with anti-CD4 FITC, anti-CD14 FITC (Beckman Coulter) and anti-CD45 PC5 followed by red blood cells lysis.
T253 5624-5781 Sentence denotes Stained cells were then washed with Dulbecco’s Phosphate Buffered Saline and permeabilized with the IntraPrep Parmeabilization Reagent kit (Beckman Coulter).
T254 5782-5857 Sentence denotes Anti-IL-6 PE (Beckman Coulter) was added and analyzed after flow cytometry.
T255 5858-6007 Sentence denotes Peripheral blood mononuclear cells (PBMCs) were isolated after gradient centrifugation over Ficoll (Biochrom, Berlin, Germany) for 20 min at 1,400 g.
T256 6008-6133 Sentence denotes After three washings in ice-cold PBS pH 7.2, PBMCs were counted in a Neubauer plate with trypan blue exclusion of dead cells.
T257 6134-6350 Sentence denotes They were then diluted in RPMI 1640 enriched with 2mM of L-glutamine, 500 μg/mL of gentamicin, 100 U/mL of penicillin G, 10 mM of pyruvate, 10% fetal bovine serum (Biochrom) and suspended in wells of a 96-well plate.
T258 6351-6423 Sentence denotes The final volume per well was 200 μL with a density of 2 × 106 cells/mL.
T259 6424-6514 Sentence denotes PBMCs were exposed in duplicate for 24 h or 5 days at 37°C in 5% CO2 to different stimuli:
T260 6515-6736 Sentence denotes 10 ng/mL of Escherichia coli O55:B5 lipopolysaccharide (LPS, Sigma, St. Louis, USA); 5 × 105 colony forming units of heat-killed Candida albicans; 25% of patient plasma; or 10 μg/mL of Tocilizumab (Roche, Athens, Greece).
T261 6737-6806 Sentence denotes After incubation, cells were removed and analyzed for flow cytometry.
T262 6807-6986 Sentence denotes Concentrations of TNFα, IL-1β, IL-6, IL-17A and IFNγ were measured in cell supernatants and/or serum in duplicate by an enzyme immunoassay (Invitrogen, Carlsbad, California, USA).
T263 6987-7143 Sentence denotes The lowest detections limits were as follows: for TNF-α, 40 pg/mL; for IL-1β, 10 pg/mL; for IL-6, 10 pg/mL; for IL-17A, 10 pg/mL; and for IFN-γ, 12.5 pg/mL.
T264 7144-7306 Sentence denotes Concentrations of ferritin were measured in serum by an enzyme-immunoassay (ORGENTEC Diagnostika GmbH, Mainz, Germany); the lower limit of detection was 75 ng/mL.
T265 7307-7504 Sentence denotes Six patients with immune dysregulation were treated with single intravenous infusion of 8 mg/kg of Tocilizumab (RoAcremra, Roche) based on the National Health Care off-label provision for COVID-19.
T266 7505-7590 Sentence denotes Absolute lymphocyte blood counts were compared before and after Tocilizumab infusion.
T267 7592-7631 Sentence denotes Quantification and Statistical Analysis
T268 7632-7748 Sentence denotes Qualitative data were presented as percentages and confidence intervals (CIs) and compared by the Fisher exact test.
T269 7749-7957 Sentence denotes Qualitative data were presented as mean and standard deviation and compared by the Student’ s “t-test”; they were presented as mean and standard error and compared by the Mann-Whitney U test for small groups.
T270 7958-8022 Sentence denotes Paired comparisons were done by the Wilcoxon’s rank-signed test.
T271 8023-8083 Sentence denotes Non-parametric correlations were done according to Spearman.
T272 8084-8137 Sentence denotes Any value of p below 0.05 was considered significant.